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oushujun / LTR_retriever

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5813529/
GNU General Public License v3.0
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xxx.genome.defalse is empty and the soft seems aborted #106

Closed zouxq97 closed 2 years ago

zouxq97 commented 2 years ago

Hi, shujun Thanks for your nice peration and maintenance for LTR_retriever software.I have performed the software and very smoothly in other species until now.But when I operated in a new species and I suffered a problem in prossess.When the log file showed that 'Modules 2-5: Start to analyze the structure of candidates...'，I found the output file xxx.genome.defalse in this step were empty.And then I checked the procedure that I ran,there were many '[perl] ' procedure.But time went away,the procedure still didn't continue and the output file was still empty. I don't know what has happened and how to deal with.

I will appreciate it If you could supply any suggestions.

oushujun commented 2 years ago

Hi, what version of LTR_retriever you are using? - Shujun

zouxq97 commented 2 years ago

Hi, what version of LTR_retriever you are using? - Shujun

The software version I am using is ltr_retriever-2.9.0-0

zouxq97 commented 2 years ago

Info update for you!I adjusted the number of threads to the minimum, and then found that the program is running normally, it may be that there is a problem with multi-threaded parallelism, thank you for your attention and feedback.

oushujun commented 2 years ago

Thanks for your feedback. Maybe your perl is not set up to use multiple processors. You may create a new conda environment and install a new perl and new LTR_retriever in the environment. - Shujun